Related papers: Long range correlations in DNA : scaling propertie…
Charge transfer can take place along double helical DNA over distances as long as 30 nanometers. However, given the active role of the thermal environment surrounding charge carriers in DNA, physical mechanisms driving the transfer process…
We study the energy structure and the transfer of an extra electron or hole along periodic polymers made of $N$ monomers, with a repetition unit made of $P$ monomers, using a Tight-Binding wire model, where a site is a monomer (e.g., in…
We call {\it monomer} a B-DNA base-pair and examine, analytically and numerically, electron or hole oscillations in monomer- and dimer-polymers, i.e., periodic sequences with repetition unit made of one or two monomers. We employ a…
We study random heteropolymer chain with gaussian distribution of kinds of monomers. The long-range correlations between kinds of monomers were introduce. The mean-field analysis of such heteropolymer indicates the existence of infinite…
Recent experiments indicated that disorder effect in DNA may lead to a transition of the charge transport mechanism from band resonant tunnelling to thermal activated hopping. In this letter, based on Mott's variable-range hopping theory we…
We use nucleosome maps obtained by high-throughput sequencing to study sequence specificity of intrinsic histone-DNA interactions. In contrast with previous approaches, we employ an analogy between a classical one-dimensional fluid of…
We present a theory of non-equilibrium long range charge transfer between donor and acceptor centers in a model polymer mediated by magnetic exciton (Kondo) bound states. Our model produces electron tunneling lengths easily exceeding…
We investigate the electron (hole) transport through short double-stranded DNA wires in which the electrons are strongly coupled to the specific vibrational modes (vibrons) of the DNA. We analyze the problem starting from a tight-binding…
The flexibility of short DNA chains is investigated via computation of the average correlation function between dimers which defines the persistence length. Path integration techniques have been applied to confine the phase space available…
The influence of decoherence and bonding on the linear conductance of single double-stranded DNA molecules is examined by fitting a phenomenological statistical model developed recently (EPJB {\bf 68}, 237 (2009)) to experimental results.…
We consider the task of detecting regulatory elements in the human genome directly from raw DNA. Past work has focused on small snippets of DNA, making it difficult to model long-distance dependencies that arise from DNA's 3-dimensional…
We study the interplay of intrinsic-electronic and environmental factors on long-range charge transport across molecular chains with up to $N\sim 80$ monomers. We describe the molecular electronic structure of the chain with a tight-binding…
DNA pattern matching is essential for many widely used bioinformatics applications. Disease diagnosis is one of these applications, since analyzing changes in DNA sequences can increase our understanding of possible genetic diseases. The…
The interplay between coherence and system-environment interactions is at the basis of a wide range of phenomena, from quantum information processing to charge and energy transfer in molecular systems, biomolecules, and photochemical…
It is shown that in a Holstein molecular chain placed in a strong longitudinal electric field some new types of excitations can arise. This excitations can transfer a charge over large distance (more than 1000 nucleotide pairs) along the…
We study theoretically the spatial correlations between the intensities measured at the input and output planes of a disordered scattering medium. We show that at large optical thicknesses, a long-range spatial correlation persists and…
We investigate the charge transfer characteristics of one and two excess charges in a DNA base-pair dimer using a model Hamiltonian approach. The electron part comprises diagonal and off-diagonal Coulomb matrix elements such a correlated…
In the human genomes, recombination frequency between homologous chromosomes during meiosis is highly correlated with their physical length while it differs significantly when their coding density is considered. Furthermore, it has been…
We consider a prototype polyene chain: donor-$\pi$(bridge)-acceptor. The distance between the donor and the acceptor is varied by increasing the number of bridged atoms and rate of electron transfer, k$_{et}$ is studied for a series of…
Charge transfer along the base-pair stack in DNA is modeled in terms of thermally-assisted tunneling between adjacent base pairs. Central to our approach is the notion that tunneling between fluctuating pairs is rate-limited by the…